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Ontologies in Physical Science
- 1. Ontologies in Physical Science Peter Murray-Rust, University of Cambridge & Open Knowledge Foundation Onto Workshop, ed.ac.uk 2013-04-11 An #animalgarden production
- 2. PMR and friends want us to help build Is it an a computational important chemistry ontology problem? $1,000,000,000/yr for compchem They need OWL Problem: How to build ontologies when people are uninterested or antagonistic even though we have the technology
- 3. Perhaps the chemists could use OWL-DL Chemists don’t use ontologies Top-down schemas like AniML haven’t (yet) taken off
- 4. Are there any ontologies in physical science that work? Crystallo- graphers build CIF dictionaries The IUCr, right? Tell us about CIF IUCr: International Union of Crystallography
- 5. CIF Core defines 500 common concepts Like the wavelength of the radiation used Or the volume of the crystal cell CIF: http://www.iucr.org/cif
- 6. An Core dictionary (coreCIF) version 2.4.3 example _diffrn_ambient_temperature ? Definition: The mean temperature in kelvins at which the intensities were measured. Range: 0.0 -> infinity Type: numb ID For machines: Constraint + type For humans http://www.iucr.org/__data/iucr/cifdic_html/1/ cif_core.dic/Idiffrn_ambient_temperature.html
- 7. Definition: The mean temperature in kelvins at which the intensities were measured. So everyone converts temperatures to use K? Yes! today I swam at 273K But chemists We MUST want to use all have a units sorts of ontology different units
- 8. OWL? Is CIF a proper ontology? It’s not RDF… …but we’ve global URIs, like cif:_diffrn_ambient_temperature Because IUCr controls the namespace prefix: cif= http://www.iucr.org/cif
- 9. CIF had 20 years of community involvement through IUCr But most top- down chemistry projects don’t work So we’ll do this bottom-up.
- 10. Every compchem program uses basically the same scientific concepts We think each should build its own dictionary so we understand the output Won’t that just be a mess? No. It’s the first step to interoperability.
- 11. The programs will use CML* for chemical output Hyperchem builds ITS dictionary NWChem Each annotates builds ITS their own dictionary program output Chemical Markup Language PMR/Rzepa http://www.xml-cml.org
- 12. Alpha-electrons: Hyperchem uses hchem:e_alpha NWChem has nwchem:_alpha_elec We agree they are the same so create compchem:alphae in a communal cml:compchem dictionary that everyone uses
- 13. What if the data structure or concepts CML provides don’t map conventions so each group can define their data structure Data can then be machine validated against each convention!
- 14. But there are We’ve over 20 prototyped with program many before. codes. They’ll be encouraged GULP, DPOL Y, CASTEP, S IESTA, MOPA C… I think it’s going to work. BUT TTT* TTT: Things Take Time (Piet Hein)
- 15. Will it work? It National labs depends on CSIRO/AU people and PNNL/US are committed And we have companies like I wish we had Hyperchem some and Kitware publishers
- 16. We’ll need tools We’ve got FoX* for FORTRAN output JUMBOTemplates to parse logfiles RDF for navigating dictionaries FoX*: XML/FORTRAN Toby White, Andrew Walker
- 17. Benefits of semantic dictionaries: • FORTRAN logfile can be made semantic • High degree of interoperability in chemistry • Semantic publication (HTML5, CML, MathML) • Interoperates with mainstream Web • Easily scalable to other phys sci. Problems: • Closed code/minds is short-term market advantage • Non-trivial commitment (updates, code revision) • Getting top-down approval (e.g. IUPAC)
- 18. Benefits of semantic dictionaries: • FORTRAN logfile can be made semantic • High degree of interoperability in chemistry • Semantic publication (HTML5, CML, MathML) • Interoperates with mainstream Web • Easily scalable to other phys sci. Problems: • Closed code/minds is short-term market advantage • Non-trivial commitment (updates, code revision) • Getting top-down approval (e.g. IUPAC)
- 19. Benefits of semantic dictionaries: • FORTRAN logfile can be made semantic • High degree of interoperability in chemistry • Semantic publication (HTML5, CML, MathML) • Interoperates with mainstream Web • Easily scalable to other phys sci. Problems: • Closed code/minds is short-term market advantage • Non-trivial commitment (updates, code revision) • Getting top-down approval (e.g. IUPAC)
- 20. Benefits of semantic dictionaries: • FORTRAN logfile can be made semantic • High degree of interoperability in chemistry • Semantic publication (HTML5, CML, MathML) • Interoperates with mainstream Web • Easily scalable to other phys sci. Problems: • Closed code/minds is short-term market advantage • Non-trivial commitment (updates, code revision) • Getting top-down approval (e.g. IUPAC)
- 21. Benefits of semantic dictionaries: • FORTRAN logfile can be made semantic • High degree of interoperability in chemistry • Semantic publication (HTML5, CML, MathML) • Interoperates with mainstream Web • Easily scalable to other phys sci. Problems: • Closed code/minds is short-term market advantage • Non-trivial commitment (updates, code revision) • Getting top-down approval (e.g. IUPAC)
- 22. Perhaps the chemists could use OWL-DL Chemists don’t use ANY ontologies Top-down schemas like AniML haven’t (yet) taken off